Variant report

Variant	rs4465771
Chromosome Location	chr2:111809030-111809031
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10187034	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11123325	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13000374	0.91[CHD][hapmap];0.84[JPT][hapmap]
rs1821969	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1898846	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2880119	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4848374	1.00[CEU][hapmap];0.87[CHB][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4849360	1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6759108	0.86[CEU][hapmap];0.80[CHB][hapmap];0.83[CHD][hapmap];0.96[GIH][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874838	chr2:111376870-112046226	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv874839	chr2:111400934-111868010	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4465771	JHDM1D	trans	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:111787800-111825400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr2:111806600-111813400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
3	chr2:111806800-111809800	Enhancers	Primary B cells from peripheral blood	blood
4	chr2:111806800-111810600	Enhancers	Primary T cells from cord blood	blood
5	chr2:111807000-111809200	Enhancers	Primary B cells from cord blood	blood
6	chr2:111807200-111810000	Enhancers	GM12878-XiMat	blood
7	chr2:111807200-111812600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr2:111807800-111809200	Enhancers	Primary T cells fromperipheralblood	blood
9	chr2:111807800-111810400	Weak transcription	Fetal Heart	heart
10	chr2:111807800-111811600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:111808200-111812400	Weak transcription	Fetal Kidney	kidney
12	chr2:111808400-111812600	Weak transcription	Pancreas	Pancrea
13	chr2:111808400-111812800	Weak transcription	Thymus	Thymus
14	chr2:111808600-111811600	Weak transcription	Fetal Thymus	thymus
15	chr2:111808600-111812800	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr2:111808800-111811600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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